issues
search
KarrLab
/
wc_sim
A multi-algorithmic simulator for whole-cell models
MIT License
6
stars
2
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
dFBA submodels
#65
artgoldberg
closed
3 years ago
1
Misc
#64
artgoldberg
opened
4 years ago
0
Improve dynamic tests
#63
artgoldberg
opened
4 years ago
5
Give abstract compartments control over their volumes
#62
artgoldberg
closed
4 years ago
1
Select Stop Condition(s) to execute
#61
artgoldberg
opened
4 years ago
0
Integrate ODEs, SBML test suite, and other code from fall 2018 wc_sim branch
#60
artgoldberg
closed
4 years ago
4
Combine `DynamicSpecies` with the local species population
#59
artgoldberg
closed
4 years ago
1
Dynamic dFBA expressions
#58
artgoldberg
closed
3 years ago
1
Replace normal with single-tailed distribution(s) for initializing non-negative values
#57
artgoldberg
opened
4 years ago
1
Separate the initialization of simulation state from the construction of simulation objects
#56
artgoldberg
closed
3 years ago
1
Properly initialize the multi-algorithmic simulator
#55
artgoldberg
closed
4 years ago
0
move phold.py to de_sim
#54
artgoldberg
closed
4 years ago
2
capture output generated by testing
#53
artgoldberg
closed
4 years ago
1
Speed up wc_sim tests
#52
artgoldberg
closed
3 years ago
2
Failure to validate reading of examples/translation_metabolism_hybrid_model/model.xlsx
#51
artgoldberg
closed
4 years ago
3
Error if model has no sub-models
#50
artgoldberg
closed
4 years ago
2
Simulation results should be logged to the specified directory rather than a subdirectory whose name is the date
#48
jonrkarr
closed
4 years ago
1
Remove `wc_sim.log` which is redundant with `RunResults`
#47
jonrkarr
closed
4 years ago
1
Consider merging `dynamic_component` and `dynamic_expression` modules
#46
jonrkarr
closed
4 years ago
0
Move `get_species_and_compartment_from_name` to wc_lang.Species
#45
jonrkarr
closed
4 years ago
1
Consider merging `wc_sim.multialgorithm.dynamic_expressions.DynamicExpression.prepare` with expression parsing in `obj_model.expression`
#43
jonrkarr
closed
4 years ago
4
Separate all code for testing into a separate test module
#42
jonrkarr
closed
4 years ago
1
Sample from new distributions of initial conditions
#41
jonrkarr
closed
4 years ago
3
Add integration tests for different mass dynamics schemes
#49
jonrkarr
closed
5 years ago
1
Address issues noted in wc_lang.expression_utils
#40
jonrkarr
closed
4 years ago
2
stop recording history in LocalSpeciesPopulation; checkpointing is a better approach
#39
artgoldberg
closed
5 years ago
1
Improve ODE submodels
#38
artgoldberg
opened
5 years ago
0
re-enable Mass Action in DynamicRateLaw.eval()
#37
artgoldberg
closed
5 years ago
1
loosen 'time of previous _record_history() ({}) not less than current time ({})'
#36
artgoldberg
closed
5 years ago
0
Handle rate laws with k_cat but no k_M
#35
artgoldberg
closed
5 years ago
1
Support dynamic compartment volumes
#34
jonrkarr
closed
4 years ago
5
Remove compartment attribute from submodels
#33
jonrkarr
closed
5 years ago
1
Implement sampling of initial conditions
#32
jonrkarr
closed
5 years ago
1
Speed up RunResults
#31
jonrkarr
closed
4 years ago
2
Store computed volumes and masses for all compartments
#30
jonrkarr
closed
5 years ago
1
Submodels with no reactions or no propensity generate a large number of events
#29
jonrkarr
closed
4 years ago
1
Propensities to run_results
#28
szb37
closed
3 years ago
3
Compute reaction rates in abundance space
#26
artgoldberg
closed
5 years ago
2
Make MW>0 check optional
#25
artgoldberg
closed
4 years ago
2
Add perturbation events
#24
artgoldberg
opened
6 years ago
0
specify seed for random number generators
#23
artgoldberg
closed
6 years ago
2
Avoid usage of obj_model.Model.Manager.get_one which lacks the context of a specific model
#22
jonrkarr
closed
6 years ago
1
sim results should be stored in the specified directory rather than a subdirectory with a timestep
#21
jonrkarr
closed
5 years ago
1
Enable restart of a simulation from a checkpoint or RunResults
#20
artgoldberg
opened
6 years ago
1
record metadata about all the code used
#19
artgoldberg
closed
3 years ago
1
"python wc_sim sim --help" doesn't work
#18
artgoldberg
closed
6 years ago
0
Integrate wc_sim.multialgorithm.wc_simulate with cement CLI
#17
jonrkarr
closed
6 years ago
1
Support new units attribute of `wc_lang.Concentration`
#16
jonrkarr
closed
6 years ago
1
downstream dependence + relation to old_wc_sim
#15
szb37
closed
5 years ago
4
simple example of an SSA simulation
#14
artgoldberg
closed
6 years ago
2
Previous
Next